cpvSNP

Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

Bioconductor version: 3.24 · Package version: 1.45.0

Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cpvSNP")